scmap-shiny

This is a shiny implementation of the scmap R package for projection of cells from a scRNA-Seq experiment to either another scRNA-Seq dataset or to a collection of multiple datasets indexes.

Indexes

To be able to use the scmap-shiny with your own dataset indexes you just need to substitute our references with yours in the www folder.

To create your own indexes please install scmap using:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scmap")

Then use the indexCluster or indexCell methods to create your indexes.

Running locally

To install and run scmap-shiny locally just clone this repository using:

git clone https://github.com/hemberg-lab/scmap-shiny.git

Then open it with RStudio and run the Shiny application.

Running on a Cloud

To run scmap-shiny on a Cloud please create a Docker image of it using the Dockerfile provided. Once the image is ready it can be run either locally or on a Cloud.

We have built our own image of scmap-shiny using quay.io. To run it locally:

docker run --rm -p 3838:3838 quay.io/hemberg-group/scmap-shiny

Then scmap-shiny will be accessible at http://localhost:3838/scmap/

To run in a detached mode on the Cloud:

docker run -d -p 80:3838 quay.io/hemberg-group/scmap-shiny

Then scmap-shiny will be accessible at http://YOUR_CLOUD_IP/scmap/.

Alternatively, you can manually install a Shiny server on your instance and all corresponding R packages mentioned in the Dockerfile. You will also need to copy your scmap-shiny files to /srv/shiny-server/scmap folder.